Find research datasets worth reusing

opencc-by-4.0Oct 2021View details →

Activity cliffs with dual-atom replacements and single-atom analogs

From the ChEMBL database, 852 activity cliffs (ACs) with dual-atom replacements were extracted which were formed by compounds with high-confidence activity data. Each AC captured an at least 10-fold difference in compound potency. For a subset of these ACs, analogs with corresponding single-atom replacements were identified. The dual-atom ACs and available single-atom replacement analogs were provided (SMILES representation and ChEMBL compound ID). For each AC compound and analog, targets from ChEMBL are reported (with UniProt ID). The target shared by all associated compounds represents the primary AC target

opencc-by-4.0Nov 2021View details →

Supporting data for: "Data-driven discovery of cardiolipin-selective small molecules by computational active learning"

This repository contains supporting data and code for the paper titled "Data-driven discovery of cardiolipin-selective small molecules by computational active learning" by Bernadette Mohr, Kirill Shmilovich, Isabel Kleinwächter, Dirk Schneider, Andrew L.Ferguson, and Tristan Bereau.

opencc-zeroNov 2021View details →

Dataset for "Study of 72 pulsars discovered in the PALFA survey: Timing analysis, glitch activity, emission variability, and a pulsar in an eccentric binary"

This repository includes TEMPO-readable ephemerides associated with the final timing solutions presented in Table 3 (text-readable format; .par files) of the manuscript, "Study of 72 pulsars discovered in the PALFA survey: Timing analysis, glitch activity, emission variability, and a pulsar in an eccentric binary" accepted to the Astrophysical Journal (October 2021).

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Raw microscopy data from: Endoplasmic reticulum stress activates human IRE1α through reversible assembly of inactive dimers into small oligomers

Protein folding homeostasis in the endoplasmic reticulum (ER) is regulated by a signaling network, termed the unfolded protein response (UPR). Inositol-requiring enzyme 1 (IRE1) is an ER membrane-resident kinase/RNase that mediates signal transmission in the most evolutionarily conserved branch of the UPR. Dimerization and/or higher-order oligomerization of IRE1 are thought to be important for its activation mechanism, yet the actual oligomeric states of inactive, active, and attenuated mammalian IRE1 complexes remained unknown. We developed an automated two-color single-molecule tracking approach to dissect the oligomerization of tagged endogenous human IRE1 in live cells. In contrast to previous models, our data indicate that IRE1 exists as a constitutive homodimer at baseline and assembles into small oligomers upon ER stress. We demonstrate that the formation of inactive dimers and stress-dependent oligomers is fully governed by IRE1's lumenal domain. Phosphorylation of IRE1's kinase domain occurs more slowly than oligomerization and is retained after oligomers disassemble back into dimers. Our findings suggest that assembly of IRE1 dimers into larger oligomers specifically enables trans- autophosphorylation, which in turn drives IRE1's RNase activity.

opencc-zeroNov 2021View details →

opencc-by-4.0Sep 2021View details →

SynActJ: Easy-to-use automated analysis of synaptic activity

Neuronal synapses are highly dynamic communication hubs that mediate chemical neurotransmission via the exocytic fusion and subsequent endocytic recycling of neurotransmitter-containing synaptic vesicles (SVs). Functional imaging tools allow for the direct visualization of synaptic activity by detecting action potentials, pre- or postsynaptic calcium influx, SV exo- and endocytosis, and glutamate release. Fluorescent organic dyes or synapse-targeted genetic molecular reporters, such as calcium, voltage or neurotransmitter sensors and synapto-pHluorins reveal synaptic activity by undergoing rapid changes in their fluorescence intensity upon neuronal activity on timescales of milliseconds to seconds, which typically are recorded by fast and sensitive widefield live cell microscopy. The analysis of the resulting time-lapse movies in the past has been performed by either manually picking individual structures, custom scripts that have not been made widely available to the scientific community, or advanced software toolboxes that are complicated to use. For the precise, unbiased and reproducible measurement of synaptic activity, it is key that the research community has access to bio-image analysis tools that are easy-to-apply and allow the automated detection of fluorescent intensity changes in active synapses. Here we present SynActJ (Synaptic Activity in ImageJ), an easy-to-use fully open-source workflow that enables automated image and data analysis of synaptic activity. The workflow consists of a Fiji plugin performing the automated image analysis of active synapses in time-lapse movies via an interactive seeded watershed segmentation that can be easily adjusted and applied to a dataset in batch mode. The extracted intensity traces of each synaptic bouton are automatically processed, analyzed, and plotted using a R Shiny workflow. We validate the workflow on time-lapse images of stimulated synapses expressing the presynaptic pH reporter Synaptophysin-pHluorin or a synapse-targeted calcium sensor, Synaptophysin-RGECO. We compare the automatic workflow to manual analysis and compute calcium-influx and SV exo-/ endocytosis kinetics and other parameters for synaptic vesicle recycling under different conditions. We predict SynActJ to become an important tool for the analysis of synaptic activity and synapse properties.

Preliminary neutron data for cryotrapping peroxide in the active site of human mitochondrial manganese superoxide dismutase crystals for neutron diffraction

The files are preliminary refined neutron coordinates and data on a cryotrapped peroxo species at the active site of human manganese superoxide dismutase crystals.

opencc-by-4.0May 2021View details →

Fig. 1 in Joaquim José da Silva (c. 1755-1810): his life, natural history collecting activities, and involvement in the so-called first scientific expedition in the interior of Angola

Fig. 1. – "Aspecto da embocadura do Rio Dande" [Aspect of the mouth of the River Dande] with Joaquim José da Silva (left) and José António (right). [a. "Forno da cal" [lime oven]; b. "Armazem de a-guardar" [storage]; c. "Sanzallas" [dwellings]; d. "Armazem da madeira" [timber storage]; e. "Igreja que foi dos Jesuitas" [church that was of the Jesuits]; f. "Ponta do Mussule(?)" [Mussule(?) Tip] [SILVA, J.J. (post. 1785: fig. 84); painting executed by José António] [© Arquivo Histórico dos Museus da Universidade de Lisboa]

opencc-by-4.0May 2021View details →

Fig. 2 in Joaquim José da Silva (c. 1755-1810): his life, natural history collecting activities, and involvement in the so-called first scientific expedition in the interior of Angola

Fig. 2. – Itinerary of Joaquim José da Silva in Angola from 1783 to 1810 according to TEIXEIRA (1962) in pink, SIMON (1983) in blue, and this work in red.

opencc-by-4.0Feb 2022View details →

UPF3A and UPF3B are redundant and modular activators of nonsense-mediated mRNA decay in human cells

Source data for the publication: UPF3A and UPF3B are redundant and modular activators of nonsense-mediated mRNA decay in human cells. Includes raw image data (e.g. agarose gels, western blots, northern blots), quantifications, qPCR raw Ct values and other supporting material.

opencc-by-4.0Feb 2021View details →

Fig. 1 in Individual Movement Of Large Carabids As A Link For Activity Density Patterns In Various Forestry Treatments

Fig. 1. Mean activity density of Carabus scheidleri (a) and C. coriaceus (b) per sampling plot in different for- estry treatments (C = control, CC = clear-cutting, P = preparation cut- ting) between 2014 and 2018. Verti- cal lines represent a 95% confidence interval and capital letters above bars indicate significant differences based on Tukey's multiple compari- sons of means

opencc-by-4.0Feb 2021View details →

Fig. 2 in Individual Movement Of Large Carabids As A Link For Activity Density Patterns In Various Forestry Treatments

Fig. 2. Movements of Carabus scheidleri (a) within and between forestry treatments (C = control, CC = clear-cutting, P = preparation cutting) based on CMR. The number next to the arrow corresponds with the number of recorded movements. Individual trajectories of radio-tracked C. coriaceus (b) in the experimental area, black dots represent the first release point for each trajectory

Crosswalks IUCLID 6.6 EU PPP Microorganisms - active substance application (product) to KMA&KMP

This Excel file provides detailed crosswalks from the <a href="https://esubmission.ecpa.eu/toc/EU">EU Table of Contents (SANCO/10181/2013)</a> for microbial plant protection product (PPP) dossiers to <a href="https://iuclid6.echa.europa.eu/">IUCLID 6.6</a>. It includes two spreadsheets, containing the mappings for active substance (as laid out in Commission Regulation (EU) No 283/2013) and representative product (Commission Regulation (EU) No 284/2013): <ul> <li>EU_PPP_Micro_ActiveSubstance: mapping between the "KMA" ToC and IUCLID 6.5's working context "EU PPP Microorganisms - active substance information"</li> <li>EU_PPP_Micro_Product: mapping between the "KMP" ToC and IUCLID 6.5's working context "EU PPP Microorganisms - active substance application (product)"</li> </ul> The spreadsheets map each section of the original EU ToC to: <ul> <li>IUCLID section: name of the section in IUCLID where to input the corresponding data/information</li> <li>Endpoint study record: name of the document template used to report individual studies of the section (if exists). These usually correspond to OECD Harmonised Templates (OHT).</li> <li>Endpoint summary: name of the document template used to report the summary information of the studies presented in the section (if exists)</li> <li>Other IUCLID document: name of any other document template in IUCLID used to report information of the section (if exists)</li> <li>OHT: name/id of the OECD Harmonised Template used for the endpoint study record document (if exists)</li> <li>Additional context: fulI IUCLID paths indicating the section of the respective document where information needs to be provided and/or specific values to be indicated. If more than one path is provided, these are separated by ";". Operators "=" and "!=" are used to indicate values to be used and to be avoided, respectively. When more than one value is possible, "IN" and "NOT IN" operators are used, followed by the exhaustive list of possible values. This nomenclature was defined with the aim of making contents machine-readable.</li> </ul> Version 3 includes changes in the table of contents of IUCLID6.6.

Data and code from: "A transcriptional rheostat couples past activity to future sensory responses" (Tsukahara, Brann, et al. 2021 Cell)

# A transcriptional rheostat couples past activity to future sensory responses Code and data to replicate analyses in Tsukahara, Brann et al. 2021 Cell <a href="https://doi.org/10.1016/j.cell.2021.11.022">https://doi.org/10.1016/j.cell.2021.11.022</a> ## Summary Animals traversing different environments encounter both stable background stimuli and novel cues, which are thought to be detected by primary sensory neurons and then distinguished by downstream brain circuits. Here we show that each of the ~1000 olfactory sensory neuron (OSN) subtypes in the mouse harbors a distinct transcriptome whose content is precisely determined by interactions between its odorant receptor and the environment. This transcriptional variation is systematically organized to support sensory adaptation: expression levels of more than 70 genes relevant to transforming odors into spikes continuously vary across OSN subtypes, dynamically adjust to new environments over hours, and accurately predict acute OSN-specific odor responses. The sensory periphery therefore separates salient signals from predictable background via a transcriptional rheostat whose moment-to-moment state reflects the past and constrains the future; these findings suggest a general model in which structured transcriptional variation within a cell type reflects individual experience. ## Manuscript For more details, please see our Open Access manuscript: <a href="https://www.cell.com/cell/fulltext/S0092-8674(21)01337-4">https://www.cell.com/cell/fulltext/S0092-8674(21)01337-4</a> # Code 1. The code here is a copy of that on GitHub: <a href="https://github.com/dattalab/Tsukahara_Brann_OSN">https://github.com/dattalab/Tsukahara_Brann_OSN</a>. Instructions for how to download and install it can be found in the README.md file. 2. Data is available on the NCBI GEO (accession <a href="https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE173947">GSE173947</a>) and raw fastq files are available from the SRA (accession SRP318630). 3. Supplementary data (imaging traces and example preprocessed AnnData object for the home-cage dataset) can be found in the data folders of the attached Tsukahara_Brann_OSN-zenodo.zip file.

Harnessing single cell RNA sequencing to identify dendritic cell types, characterize their biological states and infer their activation trajectory

Summary: Dendritic cells (DCs) orchestrate innate and adaptive immunity, by translating the sensing of distinct danger signals into the induction of different effector lymphocyte responses, to induce different defense mechanisms suited to face distinct types of threats. Hence, DCs are very plastic, which results from two key characteristics. First, DCs encompass distinct cell types specialized in different functions. Second, each DC type can undergo different activation states, fine-tuning its functions depending on its tissue microenvironment and the pathophysiological context, by adapting the output signals it delivers to the input signals it receives. Hence, to better understand DC biology and harness it in the clinic, we must determine which combinations of DC types and activation states mediate which functions, and how. To decipher the nature, functions and regulation of DC types and their physiological activation states, one of the methods that can be harnessed most successfully is ex vivo single cell RNA sequencing (scRNAseq). However, for new users of this approach, determining which analytics strategy and computational tools to choose can be quite challenging, considering the rapid evolution and broad burgeoning of the field. In addition, awareness must be raised on the need for specific, robust and tractable strategies to annotate cells for cell type identity and activation states. It is also important to emphasize the necessity of examining whether similar cell activation trajectories are inferred by using different, complementary methods. In this chapter, we take these issues into account for providing a pipeline for scRNAseq analysis and illustrating it with a tutorial reanalyzing a public dataset of mononuclear phagocytes isolated from the lungs of naïve or tumor-bearing mice. We describe this pipeline step-by-step, including data quality controls, dimensionality reduction, cell clustering, cell cluster annotation, inference of the cell activation trajectories and investigation of the underpinning molecular regulation. It is accompanied with a more complete tutorial on Github. We anticipate that this method will be helpful for both wet lab and bioinformatics researchers interested in harnessing scRNAseq data for deciphering the biology of DCs or other cell types, and that it will contribute to establishing high standards in the field.   Data: 1. negative_cDC1_relative_signatures.csv : Negative signatures for performing Connectivity Map (cMAP) Analysis 2. positive_cDC1_relative_signatures.csv : Positive signatures for performing Connectivity Map (cMAP) Analysis

opencc-zeroJan 2022View details →

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Ca2+ activity maps of astrocytes tagged by axo-astrocytic AAV transfer

Astrocytes exhibit localized Ca2+ microdomain (MD) activity thought to be actively involved in information processing in the brain. However, functional organization of Ca2+ MDs in space and time in relationship to behavior and neuronal activity is poorly understood. Here, we first show that Adeno-Associated Virus (AAV) particles transfer anterogradely from axons to astrocytes. Then we use this axo-astrocytic AAV transfer to express genetically encoded Ca2+ indicators at high contrast circuit-specifically. In combination with two-photon microscopy and unbiased, event-based analysis we investigated cortical astrocytes embedded in the vibrissal thalamocortical circuit. We found a wide range of Ca2+ MD signals, some of which were ultrafast (≤300 ms). Frequency and size of signals were extensively increased by locomotion but only subtly with sensory stimulation. The overlay of these signals resulted in behavior dependent maps with characteristic Ca2+ activity hotspots, maybe representing memory engrams. These functional subdomains are stable over days, suggesting subcellular specialization.

Dataset related to article "Complement activation promoted by the lectin pathway mediates C3aR-dependent sarcoma progression and immunosuppression"

This record contains raw data related to article “Complement activation promoted by the lectin pathway mediates C3aR-dependent sarcoma progression and immunosuppression" Complement has emerged as a component of tumor promoting inflammation. We conducted a systematic assessment of the role of complement activation and effector pathways in sarcomas. C3 -/-, MBL1/2 -/- and C4 -/- mice showed reduced susceptibility to 3-methylcholanthrene sarcomagenesis and transplanted sarcomas, whereas C1q and factor B deficiency had marginal effects. Complement 3a receptor (C3aR), but not C5aR1 and C5aR2, deficiency mirrored the phenotype of C3 -/- mice. C3 and C3aR deficiency were associated with reduced accumulation and functional skewing of tumor-associated macrophages, increased T cell activation and response to anti-PD-1 therapy. Transcriptional profiling of sarcoma infiltrating macrophages and monocytes revealed the enrichment of MHC II-dependent antigen presentation pathway in C3-deficient cells. In patients, C3aR expression correlated with a macrophage population signature and C3 deficiency-associated signatures predicted better clinical outcome. These results suggest that the lectin pathway and C3a/C3aR axis are key components of complement and macrophage-mediated sarcoma promotion and immunosuppression.

Quantitative raw data for D1.3 - "Requirements and motivations of quadruple helix stakeholders for active engagement in the Citizen Science"

This dataset presents the quantitative raw data that was collected under the H2020 INCENTIVE project for the D1.3 -  “Requirements and motivations of quadruple helix stakeholders for active engagement in the Citizen Science Hubs”. The dataset includes the answers that were provided by almost 2,000 participants from 4 pilot European countries (Greece, Lithuania, Spain, and the Netherlands) regarding the general public's perceptions, attitudes, concerns, motivational factors and obstacles with regard to participation in Citizen Science activities. The original survey questionnaire was created and disseminated through the EUSurvey platform, and data collection took place from April to June 2021. For the statistical analysis of the data and the conclusions drawn from the analysis, you can access the D1.3 - "Requirements and motivations of quadruple helix stakeholders for active engagement in the Citizen Science Hubs”. Under INCENTIVE, four Citizen Science Hubs will be established and tested during the life-span of the project in the facilities of four Research Performing and Funding Organisations (RPFOs): University of Twente (the Netherlands), Autonomous University of Barcelona (Spain), Aristotle University of Thessaloniki (Greece) and Vilnius Gediminas Technical University (Lithuania). Essentially, the Hubs will aim to bring different stakeholders together and bridge society with science under the emerging paradigm of Citizen Science, in an institutionalised way.

opencc-by-4.0May 2022View details →

Light-activated molecular machines display broad spectrum antibacterial action

TEM images of E. coli treated with 1% DMSO or 0.5x MIC of different visible light-activated molecular machines. Light-activated molecular machines (MM) are synthetic molecular structures that, following light activation, undergo successive unidirectional rotation that results in a drilling-like rapid motion that can thrust the motor through biological membranes. Transmission electron microscopy (TEM) images revealed that treatment of E. coli with 0.5x MIC of different MM (DL-654, DL-877, DL-878) followed by activation with 42.6 J cm-2 of 405 nm light resulted in substantial changes in cell morphology including the detachment of the inner membrane from the cell wall, damage to peptidoglycan, distortion of the cell surface, and formation of outer membrane vesicles, denoting membrane and periplasmic stress, that were not evident in 1% DMSO-treated and irradiated cells.

Active Travel Data

Dataset

Large surface-rupture gaps and low surface fault slip of the 2021 Mw 7.4 Maduo earthquake along a low-activity strike-slip fault, Tibetan Plateau

In this data set, Text S1 describes methods of (i) field investigation, UAV image collection and interpretation and (ii) horizontal and vertical displacement measurements. Figure S3 shows pre-event topographic expressions of the Maduo earthquake fault. Tables S1 and S2 provide measurement results of horizontal and vertical displacements, respectively. Datasets 1-4 provide the UAV flight swath, interpreted surface ruptures and secondary cracks, horizontal displacements and vertical displacements.